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- PDB-4idm: Crystal structure of the Delta-pyrroline-5-carboxylate dehydrogen... -

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Basic information

Entry
Database: PDB / ID: 4idm
TitleCrystal structure of the Delta-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis
ComponentsDelta-1-pyrroline-5-carboxylate dehydrogenase
KeywordsOXIDOREDUCTASE / pyrroline dehydrogenase / Aldehyde dehydrogenase / pyrroline-5-carboxylate dehydrogeanse / pyrroline-5-carboxylic acid / dehydrogenation
Function / homology
Function and homology information


L-glutamate gamma-semialdehyde dehydrogenase / L-glutamate gamma-semialdehyde dehydrogenase activity / L-proline catabolic process to L-glutamate / cytoplasmic side of plasma membrane / nucleotide binding / metal ion binding
Similarity search - Function
Delta-1-pyrroline-5-carboxylate dehydrogenase / : / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...Delta-1-pyrroline-5-carboxylate dehydrogenase / : / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-glutamate gamma-semialdehyde dehydrogenase / L-glutamate gamma-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsLagautriere, T. / Bashiri, G. / Baker, E.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Characterization of the proline-utilization pathway in Mycobacterium tuberculosis through structural and functional studies.
Authors: Lagautriere, T. / Bashiri, G. / Paterson, N.G. / Berney, M. / Cook, G.M. / Baker, E.N.
History
DepositionDec 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Delta-1-pyrroline-5-carboxylate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)61,5571
Polymers61,5571
Non-polymers00
Water4,017223
1
A: Delta-1-pyrroline-5-carboxylate dehydrogenase

A: Delta-1-pyrroline-5-carboxylate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)123,1132
Polymers123,1132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_556x,x-y,-z+11
Buried area8290 Å2
ΔGint-16 kcal/mol
Surface area38730 Å2
MethodPISA
2
A: Delta-1-pyrroline-5-carboxylate dehydrogenase
x 6


Theoretical massNumber of molelcules
Total (without water)369,3406
Polymers369,3406
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_666-y+1,-x+1,-z+11
crystal symmetry operation11_656-x+y+1,y,-z+11
crystal symmetry operation12_556x,x-y,-z+11
Buried area41150 Å2
ΔGint-90 kcal/mol
Surface area99910 Å2
MethodPISA
3
A: Delta-1-pyrroline-5-carboxylate dehydrogenase

A: Delta-1-pyrroline-5-carboxylate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)123,1132
Polymers123,1132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area3350 Å2
ΔGint-15 kcal/mol
Surface area43670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.945, 162.945, 96.227
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Delta-1-pyrroline-5-carboxylate dehydrogenase


Mass: 61556.621 Da / Num. of mol.: 1 / Mutation: G505D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv1187 / Production host: Mycobacterium smegmatis (bacteria) / Strain (production host): Mc2 4517
References: UniProt: I6X0K4, UniProt: O50443*PLUS, EC: 1.5.1.12
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 0.1 M Bicine/Tris pH 8.1, 12% polyethylene glycol (PEG) 1000, 12% PEG 3350, 12% 2-methyl-2,4-pentandiol (MPD), 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate and 0.03 M ammonium ...Details: 0.1 M Bicine/Tris pH 8.1, 12% polyethylene glycol (PEG) 1000, 12% PEG 3350, 12% 2-methyl-2,4-pentandiol (MPD), 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate and 0.03 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979231, 0.953698, 0.979083
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 22, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9792311
20.9536981
30.9790831
ReflectionResolution: 2.5→39.78 Å / Num. all: 26403 / Num. obs: 26403 / % possible obs: 99.7 % / Rmerge(I) obs: 0.226
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
2.5-2.6363.40.7743599198.1
7.9-39.7899.10.091959199.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHELXSphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→39.78 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.759 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STRUCTURE CONSISTS IN AN ARRANGEMENT OF ORDERED AND DISORDERED LAYERS RESULTING IN GAPS BETWEEN ORDERED MOLECULES. ALTHOUGH NO MOLECULES ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STRUCTURE CONSISTS IN AN ARRANGEMENT OF ORDERED AND DISORDERED LAYERS RESULTING IN GAPS BETWEEN ORDERED MOLECULES. ALTHOUGH NO MOLECULES ARE MODELLED WITHIN THIS EMPTY LAYER, MAD DATA FROM SEMET-PRUA CRYSTALS INDICATES THAT PROTEIN ELECTRON DENSITY EXISTS WITHING THESE GAPS AND SUGGESTS A MOTION OF THE ENTIRE LAYER.
RfactorNum. reflection% reflectionSelection details
Rfree0.20702 1335 5.1 %RANDOM
Rwork0.14428 ---
obs0.14737 25067 99.57 %-
all-25067 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.091 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.24 Å20 Å2
2--0.24 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4110 0 0 223 4333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194215
X-RAY DIFFRACTIONr_bond_other_d0.0010.023963
X-RAY DIFFRACTIONr_angle_refined_deg1.81.9495749
X-RAY DIFFRACTIONr_angle_other_deg0.86839064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5365535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57522.953193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74615600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3731536
X-RAY DIFFRACTIONr_chiral_restr0.10.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021008
LS refinement shellResolution: 2.503→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 74 -
Rwork0.154 1776 -
obs--95.9 %

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